crossing96/oncoscreening huggingface dataset:
Autopsy findings from the first known death from Severe Acute Respiratory Syndrome SARS-CoV-2 in Spain.	The new coronavirus SARS-CoV-2, first identified in Wuhan, China in December, 2019, can cause Severe Acute Respiratory Syndrome (SARS) with massive alveolar damage and progressive respiratory failure. We present the relevant autopsy findings of the first patient known to have died from COVID19 pneumonia in Spain, carried out on the 14(th) of February, 2020, in our hospital (Hospital Arnau de Vilanova-Lliria, Valencia). Histological examination revealed typical changes of diffuse alveolar damage (DAD) in both the exudative and proliferative phase of acute lung injury. Intra-alveolar multinucleated giant cells, smudge cells and vascular thrombosis were present. The diagnosis was confirmed by reverse real-time PCR assay on a throat swab sample taken during the patient's admission. The positive result was reported fifteen days subsequent to autopsy.	bladder
Metastatic Plasmacytoid Bladder Cancer Harboring a CDH-1 Mutation and Producing High Levels of CA 19-9. A Case Report and Literature Review.	BACKGROUND Plasmacytoid urothelial carcinoma (PUC) is a rare and aggressive variant of urothelial cancers. Herein, we report a patient with CDH-1 mutated PUC who presented with disseminated peritoneal metastasis and high levels of CA 19-9. CASE REPORT A 65-year-old female presented to the hospital with vomiting, obstructive jaundice, and acute renal failure. Imaging studies showed bilateral hydronephrosis, bladder wall thickening without masses, and dilation of both common bile and pancreatic ducts without pancreatic masses. Carbohydrate antigen (CA) 19-9 was elevated at >17 000 U/mL. Repeated cystoscopies demonstrated no masses within the bladder, but with nodularity and inflamed mucosa, and random biopsies were obtained and showed PUC. Ascitic fluid cytology revealed metastatic PUC. A targeted exome next-generation sequencing (NGS) revealed pathogenic mutations in TP53, CDH-1, RB1, and ARIDA1A. The patient was debilitated, and hospice care was recommended. She passed away after 2 months of her initial presentation. CONCLUSIONS PUC is a rare and aggressive histological variant of bladder cancer. Advanced stage at diagnosis and high relapse rates after treatment with cytotoxic regimens are common. At the molecular level, somatic alterations in cadherin-1 (CDH-1) gene seem to be characteristic. Exploring the molecular sphere of this disease is prudent to identify possible new therapeutic targets.	bladder
Shear Wave Elasticity Differentiation Between Low- and High-Grade Bladder Urothelial Carcinoma and Correlation With Collagen Fiber Content.	OBJECTIVES: To investigate the differences in the shear wave elasticity and collagen fiber content between low- and high-grade bladder urothelial carcinoma and study the relationship between elasticity and the content of collagen fiber. METHODS: A total of 66 patients with bladder tumors who were referred to our hospital underwent transrectal or transvaginal conventional ultrasound and shear wave elasticity examinations. After bladder urothelial carcinoma was pathologically confirmed, 34 cases of low-grade and 32 cases of high-grade carcinoma were enrolled. The specimens underwent Masson trichrome staining, and image-processing software was used to quantitatively analyze the area of collagen fiber. RESULTS: Based on conventional ultrasound, the low- and high-grade groups were similar in the number, location, interior echoes, basal portion, size, and vascularity (P > .05); nevertheless, the difference in the surface condition (smooth or rough) was statistically significant (P = .03). The high-grade group had significantly higher maximum and mean elasticity than the low-grade group (P < .01). The percentage of the collagen fiber area in the high-grade group was significantly higher than that in the low-grade group (mean ± SD, 11.45% ± 1.66% versus 7.64% ± 0.70%; P = .01). There was a positive correlation between maximum elasticity, mean elasticity, and the percentage of the collagen fiber area (r = 0.75 and 0.52, respectively; P < .01). CONCLUSIONS: Shear wave elasticity can be used to differentiate between low- and high-grade bladder urothelial carcinoma. The elasticity of lesions has a close correlation with the content of collagen fiber, which may have an important impact on tissue stiffness and the development of bladder cancer.	bladder
Benefits of robotic cystectomy compared with open cystectomy in an Enhanced Recovery After Surgery program: A propensity-matched analysis.	OBJECTIVES: To compare the perioperative and oncological outcomes between robot-assisted radical cystectomy with intracorporeal urinary diversion versus open cystectomy for bladder cancer in a contemporary Enhanced Recovery After Surgery cohort. METHODS: All consecutive patients who underwent radical cystectomy and managed under an Enhanced Recovery After Surgery protocol, from December 2013 to October 2018, were reviewed. Propensity score adjustment was carried out to reduce biases attributable to covariate imbalances. RESULTS: There were 19 robot-assisted radical cystectomy with intracorporeal urinary diversion and 21 open cystectomy patients. The robot-assisted radical cystectomy with intracorporeal urinary diversion cohort was associated with lower estimated blood loss (397 vs 787 mL, P = 0.05), with a trend toward shorter duration of ileus and postoperative opioid administration. These benefits were apparent, despite a longer operative time (581 vs 446 mins, P = 0.03), a higher proportion of orthotopic bladder reconstruction (26.3 vs 9.5%, P = 0.08), a more prevalent use of neoadjuvant chemotherapy and a higher number of salvage cystectomies for the robot-assisted radical cystectomy with intracorporeal urinary diversion group. Comparable perioperative complications and length of hospital stay were observed. The pathological and intermediate oncological outcomes were similar in both groups (locally advanced disease: 52.6 vs 47.6%, P = 0.85; lymph node yield: 29 vs 34, P = 0.23). The mean recurrence-free survival and overall survival in the robot-assisted radical cystectomy with intracorporeal urinary diversion group was 37.5 and 43.0 months, respectively, compared with 21.4 (P = 0.09) and 35.5 (P = 0.14) months, respectively, in open cystectomy. CONCLUSION: Robot-assisted radical cystectomy with intracorporeal urinary diversion has perioperative benefits of lower estimated blood loss, with a trend toward faster bowel recovery and a shorter duration of opioid analgesia when compared with open cystectomy. Robot-assisted radical cystectomy with intracorporeal urinary diversion also achieves similar intermediate-term oncological and survival outcomes.	bladder
Two Immunocompromised Patients With Diffuse Alveolar Hemorrhage as a Complication of Severe Coronavirus Disease 2019.	Diffuse alveolar hemorrhage (DAH) is a severe and potentially life-threatening disease manifestation. In addition to autoimmune diseases such as antineutrophil cytoplasmic antibody-associated vasculitis and anti-glomerular basement membrane syndrome, pulmonary viral infections are known to be culprits of DAH. Health-care providers worldwide in the coronavirus disease 2019 pandemic have been confronted with an unprecedented number of viral lung infections, with great variance in symptoms and severity. Hemoptysis, the key symptom of DAH, is a rare complication. We present two cases of immunocompromised patients with rapidly developing hypoxemic respiratory failure and evidence of DAH in the context of severe acute respiratory syndrome coronavirus 2 infection.	bladder
Circulating proteomic signature for detection of biomarkers in bladder cancer patients.	The identification of clinically-relevant early diagnostic and prognostic protein biomarkers is essential to maximize therapeutic efficacy and prevent cancer progression. The aim of the current study is to determine whether aberrant plasma protein profile can be applied as a surrogate tool for early diagnosis of bladder carcinoma. Plasma samples from patients with low grade non-muscle invasive bladder cancer and healthy controls were analyzed using combined 2D-DIGE and mass-spectrometry to identify differentially expressed proteins. Validation was performed using western blotting analysis in an independent cohort of cancer patients and controls. Fifteen differentially-expressed proteins were identified of which 12 were significantly up-regulated and three were significantly down-regulated in tumors compared to controls. The Ingenuity Pathways Analysis revealed functional connection between the differentially-expressed proteins and immunological disease, inflammatory disease and cancer mediated through chemokine and cytokine signaling pathway and NF-kB transcription factor. Among the three validated proteins, haptoglobin was able to distinguish between patients with low grade bladder cancer and the controls with high sensitivity and specificity (AUC > 0.87). In conclusion, several biomarker proteins were identified in bladder cancer. Haptoglobin is a potential candidate that merit further investigation to validate its usefulness and functional significance as potential biomarkers for early detection of bladder cancer.	bladder
Open-label phase II to evaluate the efficacy of NEoadjuvant dose-dense MVAC In cOmbination with durvalumab and tremelimumab in muscle-invasive urothelial carcinoma: NEMIO.	BACKGROUND: Neoadjuvant cisplatin-based chemotherapy (NAC) is the standard of care in localized muscle-invasive bladder cancer (MIBC). However, 60-70% of patients have residual tumor after NAC. Based on the overall response rate observed in the metastatic setting, ddMVAC is the most commonly used NAC regimen in Europe. The emergence of immune checkpoint inhibitor (ICI) in the metastatic setting raises the question if the combination of chemo plus ICI could increase the pCR rate. METHODS/DESIGN: NEMIO is a French open-label randomized phase I/II trial assessing in the neoadjuvant setting the combination of ddMVAC plus durvalumab alone or with tremelimumab: 4 cycles of ddMVAC/2 weeks + 2 cycles of Durvalumab +/- Tremelimumab/4 weeks. Cystectomy is performed 4-8 weeks after the last dose of ddMVAC. Six pts will be included in each arm in a safety run-in cohort to evaluate the toxicity rate. Each arm will be expanded to a maximum of 60 pts. The primary endpoint of the safety run-in phase will be the rate of grade 3/4 treatment-related adverse events G3/4 TRAE. The primary endpoint of the phase II will be the pathological response rate and G 3/4 TRAE. Exploratory endpoints will include biomarkers of response and resistance to the combo. A total of 120 patients will be included in 15 French centers and we expect the recruitment to be completed in 2021. DISCUSSION: NEMIO trial will assess for the first time the tolerance and the efficacy of ddMVAC regimen associated with checkpoints inhibitors as neoadjuvant treatment in localized MIBC. NCT number: NCT03549715. Registered on June 8, 2018.	bladder
Epigenetic profiling demarcates molecular subtypes of muscle-invasive bladder cancer.	Muscle-invasive bladder cancer (MIBC) is a heterogeneous disease that often recurs despite aggressive treatment with neoadjuvant chemotherapy and (radical) cystectomy. Basal and luminal molecular subtypes have been identified that are linked to clinical characteristics and have differential sensitivities to chemotherapy. While it has been suggested that epigenetic mechanisms play a role in defining these subtypes, a thorough understanding of the biological mechanisms is lacking. This report details the first genome-wide analysis of histone methylation patterns of human primary bladder tumours by chromatin immunoprecipitations and next-generation sequencing (ChIP-seq). We profiled multiple histone marks: H3K27me3, a marker for repressed genes, and H3K4me1 and H3K4me3, which are indicators of active enhancers and active promoters. Integrated analysis of ChIP-seq data and RNA sequencing revealed that H3K4 mono-methylation demarcates MIBC subtypes, while no association was found for the other two histone modifications in relation to basal and luminal subtypes. Additionally, we identified differentially methylated H3K4me1 peaks in basal and luminal tumour samples, suggesting that active enhancers play a role in defining subtypes. Our study is the first analysis of histone modifications in primary bladder cancer tissue and provides an important resource for the bladder cancer community.	bladder
Practice patterns for extended venous thromboembolism chemoprophylaxis among urologic oncologists after radical cystectomy.	INTRODUCTION: Extended outpatient chemoprophylaxis (ECP) following radical cystectomy (RC) for bladder cancer is proven to reduce rates of venous thromboembolism (VTE). While ECP is commonly performed with enoxaparin, its cost-effectiveness and adherence rate has been called into question. Data from orthopedic literature suggest that ECP with direct oral anticoagulants (DOACs) may be as effective in VTE prevention as enoxaparin in patients undergoing joint surgery. Our goal is to determine how urologic oncologists employ ECP following RC. METHODS: Members of the Society of Urologic Oncology were surveyed on practice patterns for the use of ECP after RC. Specific questions were asked regarding the use of inpatient and outpatient VTE prophylaxis, as well as perceived barriers to DOACs and enoxaparin. RESULTS: There were 121 of 878 (13.8%) respondents and the majority were in academic practices (83%). Most respondents had at least 5 years of experience and performed greater than 10 cystectomies annually. Almost all participants utilized inpatient (97%) and extended (80%) chemoprophylaxis for VTE prevention. Of those who elected for ECP, almost all (96%) used enoxaparin. Only 3 respondents (3%) prescribed oral agents such as rivaroxaban (2) or warfarin (1). Among those using enoxaparin, financial-specific barriers to treatment such as lack of insurance coverage (38%), inability to afford the medication (51%), and need for additional insurance authorization (44%) were reported. Poor patient adherence and refusal to perform injections were reported by 20% and 18% of respondents, respectively. Among the 23 physicians who did not use ECP, cost (39%) and delivery method (26%) were cited as barriers to treatment. CONCLUSIONS: The majority of surveyed urologic oncologists are prescribing subcutaneous enoxaparin ECP following RC. Poor patient adherence due to self-injections and financial barriers were frequently reported and represent a possible opportunity for the use of oral anticoagulants in the post-operative setting. These data will be used in the development of a proposed clinical trial of a DOAC in the post-RC setting.	bladder
Biopsy at flexible cystoscopy: is it worthwhile?	INTRODUCTION: Flexible cystoscopy is the gold standard for diagnosis and surveillance of bladder carcinoma. Most flexible cystoscopes feature a working channel allowing for bladder biopsy and diathermy if a suspicious lesion is observed. However, the working channel permits only small instruments which limit the volume of material retrieved for histological analysis. There are no published standards for quality control of biopsy specimens taken at flexible cystoscopy. We reviewed the diagnostic yield of biopsies taken at flexible cystoscopy at our institution. METHODS: Theatre log books were retrospectively examined to identify cases of flexible cystoscopy where bladder biopsy was performed. Histopathology reports were reviewed. All biopsies were taken using single-use biopsy forceps, diameter 1.8 mm, open cup width 4.5 mm. RESULTS: From January 2014 to December 2017, a total of 143 biopsies were performed. All biopsies were taken for suspicious lesions where the differential diagnosis included malignancy. Of the 143 samples taken, 27 biopsies showed evidence of malignancy, and 9 cases were high-grade urothelial cancer. A total of 16 samples were inadequate for any histological diagnosis. All remaining samples excluded malignancy within the sample provided. A histopathological diagnosis was provided for almost 89% of cases. CONCLUSION: Approximately 18% of biopsies detected malignancy. While only small volumes of tissue are collected at flexible cystoscopy, these can help to distinguish malignancy from benign pathology. Our institution reports a non-diagnostic rate of approximately 11%, and in these cases, when there is still a suspicion of malignancy, a rigid cystoscopy and biopsy should be performed.	bladder
Sub-Staging-Specific Differences in Recurrence-Free, Progression-Free, and Cancer-Specific Survival for Patients with T1 Bladder Cancer: A Systematic Review and Meta-Analysis.	INTRODUCTION: The efficiency of the T1 sub-staging system on categorizing bladder cancer (BC) patients into subgroups with different clinical outcomes was unclear. We summarized relevant evidences, including recurrence-free survival (RFS), progression-free survival (PFS), and cancer-specific survival (CSS), to analyze the prognostic significance of T1 sub-stage. METHODS: Systematic literature searches of MEDLINE, EMBASE, and the Cochrane Library were performed. We pooled data on recurrence, progression, and CSS from 35 studies. RESULTS: The pooled hazard ratios (HRs) and 95% confidence intervals (CIs) indicated the difference in RFS between T1a sub-stage and T1b sub-stage (HR 1.28, 95% CI 1.14-1.43, p < 0.001). The significant difference was observed in PFS between the 2 arms (HR 2.18, 95% CI 1.95-2.44, p < 0.001). Worse CSS was found in T1b patients than in T1a patients (HR 1.36, 95% CI 1.21-1.54, p < 0.001). CONCLUSIONS: T1 sub-staging system based on the invasion depth into muscularis mucosae can be a significant prognostic factor for RFS, PFS, and CSS of patients with T1 BC. Urologists and pathologists are encouraged to work together to give a precise sub-stage classification of T1 BC, and T1 sub-staging system should be a routine part of any histopathological report when possible. Different treatment strategies need to be developed for both T1a BC and T1b BC.	bladder
Comparing Perioperative Complications Between Laparoscopic and Robotic Radical Cystectomy for Bladder Cancer.	Background: Minimally invasive cystectomy is being increasingly performed, however, data comparing laparoscopic radical cystectomy (LRC) and robotic radical cystectomy (RRC) are scarce. We compared 30- and 90-day Clavien-Dindo Classification (CDC) complications between patients undergoing LRC and RRC at our center. Materials and Methods: We retrospectively evaluated 300 patients who underwent minimally invasive radical cystectomy from January 2007 to July 2019 and grouped them into LRC (112 patients) and RRC (188 patients). We compared the two groups for demographic variables, perioperative characteristics, and 30- and 90-day CDC overall, minor, and major complications. Multivariable logistic regression analysis was performed to identify variables that predict perioperative complications. Results: The two groups were comparable for the duration of surgery (270 minutes in LRC vs 265 minutes in RRC) and rate of conversion to open surgery. The RRC cohort had a higher estimated blood loss (EBL) (675 mL vs 500 mL, p = 0.006), but the two groups had a comparable need for intraoperative transfusion. Patients undergoing RRC also had a shorter duration of hospital stay (13 days vs 14 days, p < 0.001). There was no difference between the two groups for 30- and 90-day CDC overall, minor, and major complications. The incidence of rehospitalization within 30 days (p = 0.1) and surgical reintervention (p = 0.5) was also comparable between the two groups. On multivariable logistic regression analysis, approach to cystectomy (RRC vs LRC) was not a significant predictor of 30-day CDC overall and major complications. Conclusion: LRC was associated with lesser EBL, whereas the hospital stay was shorter in patients undergoing RRC. The two approaches were comparable with each other for 30- and 90-day CDC overall, minor, and major complications. The choice between the two approaches should depend on availability and surgeon experience and preference, rather than any specific perioperative parameter.	bladder
Mitomycin C-induced cell cycle arrest enhances 5-aminolevulinic acid-based photodynamic therapy for bladder cancer.	BACKGROUND: Photodynamic therapy (PDT) and diagnosis (PDD) using 5-aminolevulinic acid (ALA) to control the production of the intracellular photosensitizer protoporphyrin IX (PpIX) are commonly used clinically. Previously, we demonstrated that dormant and drug-induced dormancy-like cancer cells accumulated high PpIX levels, making them sensitive to ALA-PDT. Because EAU Guidelines awarded a level of evidence of 1a to mitomycin C, the drug is widely used to treat bladder cancer. In this study, we investigated that the effect of mitomycin C-induced cell cycle arrest on porphyrin metabolism, including that induced by ALA-PDT. METHODS: T24 human urinary bladder carcinoma cells were selected for this research. T24 cells were irradiated using a light-emitting diode emitting red light for the ALA-PDT assay. Cell cycle analysis was conducted by flow cytometry using bromodeoxyuridine. Cell viability was confirmed using the MTT or colony formation assay. Furthermore, mRNA gene expression analysis was performed using our previously reported methods. RESULTS: The cell cycle of T24 cells was arrested at G2/M phase by mitomycin C. PpIX accumulation was dramatically increased by mitomycin C treatment. Cell viability after ALA-PDT was remarkably decreased by mitomycin C pretreatment. The gene expression of porphyrin transporters was consistent with the metabolic and morphological results. Finally, we confirmed that ALA-PDT combined with mitomycin C treatment exerted a long-term inhibitory effect on cell proliferation. CONCLUSION: This study demonstrated a new approach to enhance the effects of ALA-PDT using drugs that induce a dormancy-like status and upregulate porphyrin metabolism.	bladder
Does bipolar energy provide any advantage over monopolar surgery in transurethral resection of non-muscle invasive bladder tumors? A systematic review and meta-analysis.	OBJECTIVE: To provide most recent and high quality evidence concerning the comparison between monopolar and bipolar transurethral resection of non-muscle invasive bladder tumors. MATERIALS AND METHODS: Two researchers performed a systematic review of the current literature independently, to identify studies published in English language. MEDLINE, EMBASE and Cochrane Central Register of Controlled Trials and Cochrane Database of Systematic Reviews were searched from inception to 31st May 2019. The included primary endpoints of the study were: detrusor muscle sampling rates, cautery artifact occurrence among specimens and 1- or 2-year recurrence rates, overall complication rate, transfusion rate, obturator reflex and bladder perforation rates. Secondary endpoints were length of hospital stay, operation room time, hemoglobin drop, urinary tract infections, TUR-syndrome, serum sodium drop and acute urinary retention rates. RESULTS: 23 studies (14 RCTs and 9 observational) were included for qualitative and quantitative synthesis, recruiting 9815 patients in monopolar resection group and 10,112 patients in bipolar resection group (experimental). We found significant differences in favor of bipolar energy in terms of cautery artifact and length of stay with bladder perforation rates were found to be significantly better in bipolar system even though these results did not sustain when RCT's only analysis was performed. No differences were found in rates of obturator reflex (even though RCT's analysis advised differently), tumor recurrence and most of the secondary endpoints. CONCLUSIONS: Bipolar transurethral bladder tumor resection is as safe and efficient as its monopolar counterpart. Bipolar technology is related to less obturator nerve contractions and less tissue thermal artifacts during resection and may result in less hospital stay.	bladder